Dataset Open Access

SIRAH-CoV2 initiative: Membrane embedded SARS-CoV-2 ORF3a (PDB id:6XDC)

Exequiel Barrera; Pablo Garay; Florencia Klein; Matías Machado; Martín Soñora; Sergio Pantano


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    <subfield code="a">&lt;p&gt;This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of the SARS-CoV2 ORF3a&amp;nbsp;dimeric transmembrane protein&amp;nbsp;(PDB id: 6XDC, Bioassembly 1) embedded in a membrane&amp;nbsp;patch containing POPE, POPC, and POPS phospholipids in a 2:1:1 proportion.&amp;nbsp;Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in&amp;nbsp;&lt;a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00435"&gt;Barrera et al. JCTC 2019&lt;/a&gt;, adding 150 mM NaCl according to&amp;nbsp;&lt;a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953"&gt;Machado &amp;amp; Pantano JCTC 2020&lt;/a&gt;.&amp;nbsp;&lt;/p&gt;

&lt;p&gt;The files contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using&amp;nbsp;&lt;a href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152"&gt;SirahTools&lt;/a&gt;&amp;nbsp;can be found at www.sirahff.com. Additionally, &amp;nbsp;&lt;/p&gt;

&lt;p&gt;The files 6xdc_SIRAHcg_rawdata_0-2us.tar, 6xdc_SIRAHcg_rawdata_2-4us.tar, 6xdc_SIRAHcg_rawdata_4-6us.tar, 6xdc_SIRAHcg_rawdata_6-8us.tar, and 6xdc_SIRAHcg_rawdata_8-10us.tar contain&amp;nbsp;all the raw information required to visualize (on VMD), analyze,&amp;nbsp;backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing&amp;nbsp;CG trajectories using&amp;nbsp;&lt;a href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152"&gt;SirahTools&lt;/a&gt;&amp;nbsp;can be found at www.sirahff.com.&lt;/p&gt;

&lt;p&gt;Additionally, the&amp;nbsp;file&amp;nbsp;6XDC_SIRAHcg_10us_prot-memb_skip10ns.tar&amp;nbsp;contains only the protein and phospholipids&amp;acute;&amp;nbsp;coordinates, with&amp;nbsp;one frame every 10ns.&lt;/p&gt;

&lt;p&gt;To take a quick look at the trajectory:&lt;/p&gt;

&lt;p&gt;1- Untar the file 6xdc_SIRAHcg_10us_prot-memb_skip10ns.tar&lt;/p&gt;

&lt;p&gt;2- Open the trajectory on VMD using the command line:&lt;/p&gt;

&lt;p&gt;vmd 6xdc_SIRAHcg_prot-memb.prmtop 6xdc_SIRAHcg_prot-memb.ncrst 6xdc_SIRAHcg_10us_prot-memb_skip10ns.nc -e sirah_vmdtk.tcl&lt;/p&gt;

&lt;p&gt;Note that you can use normal VMD drawing methods as vdw, licorice, etc.,&amp;nbsp;and coloring by&amp;nbsp;restype, element, name, etc.&amp;nbsp;&lt;/p&gt;

&lt;p&gt;This dataset is part of the SIRAH-CoV2&amp;nbsp;initiative.&lt;/p&gt;

&lt;p&gt;For further details, please contact Exequiel Barrera&amp;nbsp;(ebarrera@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).&lt;/p&gt;</subfield>
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